QuPath H-Scoring

Hi! I’m new here and didn’t really find what I was looking for so I decided to ask.

I’m currently using QuPath but I’m really new with all of these programs.
I’m analysing CD30 and CAIX ICH slides from cHL lymph nodes. I found the way how the basic things work, like + cell counter, cell detection. These slides are stained with hematoxylin in the background and CD30, CAIX 's chromogen is DAB.

I’d like to know that how can I generate H-score to the measured annotations. These are whole slides, not TMA.

Thank you in advance!

Positive Cell detection should still generate an H-score if you use all 3 thresholds, regardless of whether it is run on a TMA or tissue.
Some information discussion thresholds here: https://petebankhead.github.io/qupath/tips/2018/03/22/setting-positive.html

Cell detection (positive, sort of) is covered here, and the box circled in blue is what you use to generate 3 thresholds for the H-score. Uncheck it.
image

Some further information on general QuPath use in an overview guide here.

1 Like

Thank you for your reply it helped so much!

I also have another question. What can I do if I open a slide, and it appears blurry in QuPath. I’ve attached an image here. The file format is *.MRXS. However the CAIX version of this slide works perfectly. CD30 is blurry like at the image here.

XXXXXX - 14578_14_CD30-1.tif (2.5 MB)

MRXS is a problematic file format due to the proprietary and non-openness of the 3DHistech. It is their decision not to support it in an open source environment. There are several other posts that go into this topic in greater depth.

The only thing I can suggest is that most mrxs files will open using the Openslide server. JPEGXR encoded files will not. Zstacks may also be a problem.



etc.

1 Like

Thank you for the fast reply, I’ll read the links you’ve provided.

1 Like